From 2bb40d91c2a549940114aba34d12ef4ffb2901c7 Mon Sep 17 00:00:00 2001
From: Sebastian Bittrich <bittrich@hs-mittweida.de>
Date: Mon, 25 Mar 2019 10:21:13 -0700
Subject: [PATCH] indention and code order
---
.../properties/utils/secondary-structure.ts | 208 +++++++++---------
1 file changed, 100 insertions(+), 108 deletions(-)
diff --git a/src/mol-model/structure/model/properties/utils/secondary-structure.ts b/src/mol-model/structure/model/properties/utils/secondary-structure.ts
index bedaa01f0..ff1ba9b4e 100644
--- a/src/mol-model/structure/model/properties/utils/secondary-structure.ts
+++ b/src/mol-model/structure/model/properties/utils/secondary-structure.ts
@@ -23,12 +23,102 @@ import { AtomicHierarchy, AtomicConformation } from '../atomic';
* - validate new ordering of secondary structure elements
*/
+ /** max distance between two C-alpha atoms to check for hbond */
+const caMaxDist = 9.0;
+
+/**
+ * Constant for electrostatic energy in kcal/mol
+ * f * q1 * q2
+ * Q = -332 * 0.42 * 0.20
+ *
+ * f is the dimensional factor
+ *
+ * q1 and q2 are partial charges which are placed on the C,O
+ * (+q1,-q1) and N,H (-q2,+q2)
+ */
+const Q = -27.888
+
+/** cutoff for hbonds in kcal/mol, must be lower to be consider as an hbond */
+const hbondEnergyCutoff = -0.5
+/** prevent extremely low hbond energies */
+const hbondEnergyMinimal = -9.9
+
export function computeSecondaryStructure(hierarchy: AtomicHierarchy,
conformation: AtomicConformation): SecondaryStructure {
// TODO use Zhang-Skolnik for CA alpha only parts or for coarse parts with per-residue elements
return computeModelDSSP(hierarchy, conformation)
}
+interface DSSPContext {
+ /** Whether to use the old DSSP convention for the annotation of turns and helices, causes them to be two residues shorter */
+ oldDefinition: boolean,
+ /** alpha-helices are preferred over 3-10 helix */
+ oldOrdering: boolean,
+ getResidueFlag: (f: DSSPType) => SecondaryStructureType,
+ getFlagName: (f: DSSPType) => String,
+
+ hierarchy: AtomicHierarchy
+ proteinResidues: SortedArray<ResidueIndex>
+ /** flags for each residue */
+ flags: Uint32Array
+ hbonds: DsspHbonds,
+
+ torsionAngles: { phi: number[], psi: number[] },
+ backboneIndices: BackboneAtomIndices,
+ conformation: AtomicConformation,
+ ladders: Ladder[],
+ bridges: Bridge[]
+}
+
+interface Ladder {
+ previousLadder: number,
+ nextLadder: number,
+ firstStart: number,
+ secondStart: number,
+ secondEnd: number,
+ firstEnd: number,
+ type: BridgeType
+}
+
+const enum BridgeType {
+ PARALLEL = 0x0,
+ ANTI_PARALLEL = 0x1
+}
+
+class Bridge {
+ partner1: number;
+ partner2: number;
+ type: BridgeType;
+
+ constructor(p1: number, p2: number, type: BridgeType) {
+ this.partner1 = Math.min(p1, p2)
+ this.partner2 = Math.max(p1, p2)
+ this.type = type
+ }
+}
+
+type DSSPType = BitFlags<DSSPType.Flag>
+namespace DSSPType {
+ export const is: (t: DSSPType, f: Flag) => boolean = BitFlags.has
+ export const create: (f: Flag) => DSSPType = BitFlags.create
+ export const enum Flag {
+ _ = 0x0,
+ H = 0x1,
+ B = 0x2,
+ E = 0x4,
+ G = 0x8,
+ I = 0x10,
+ S = 0x20,
+ T = 0x40,
+ T3 = 0x80,
+ T4 = 0x100,
+ T5 = 0x200,
+ T3S = 0x400, // marks 3-turn start
+ T4S = 0x800,
+ T5S = 0x1000
+ }
+}
+
export function computeModelDSSP(hierarchy: AtomicHierarchy,
conformation: AtomicConformation,
oldDefinition = true,
@@ -75,9 +165,7 @@ export function computeModelDSSP(hierarchy: AtomicHierarchy,
assignSheets(ctx)
const assignment = getDSSPAssignment(flags, getResidueFlag)
-
const type = new Uint32Array(hierarchy.residues._rowCount) as unknown as SecondaryStructureType[]
-
const keys: number[] = []
const elements: SecondaryStructure.Element[] = []
@@ -86,9 +174,8 @@ export function computeModelDSSP(hierarchy: AtomicHierarchy,
type[proteinResidues[i]] = assign
const flag = getResidueFlag(flags[i])
// TODO is this expected behavior? elements will be strictly split depending on 'winning' flag
- if (elements.length === 0 || // check ought to fail at very start
- flag !== (elements[elements.length - 1] as SecondaryStructure.Helix | SecondaryStructure.Sheet).flags) { // exact flag changed
- elements[elements.length] = createElement(mapToKind(assign), flags[i], getResidueFlag)
+ if (elements.length === 0 /* would fail at very start */ || flag !== (elements[elements.length - 1] as SecondaryStructure.Helix | SecondaryStructure.Sheet).flags /* flag changed */) {
+ elements[elements.length] = createElement(mapToKind(assign), flags[i], getResidueFlag)
}
keys[i] = elements.length - 1
}
@@ -133,89 +220,15 @@ function createElement(kind: string, flag: DSSPType.Flag, getResidueFlag: (f: DS
}
function mapToKind(assignment: SecondaryStructureType.Flag) {
- if (assignment === SecondaryStructureType.SecondaryStructureDssp.H || assignment === SecondaryStructureType.SecondaryStructureDssp.G ||
- assignment === SecondaryStructureType.SecondaryStructureDssp.I) {
- return 'helix'
- } else if (assignment === SecondaryStructureType.SecondaryStructureDssp.B || assignment === SecondaryStructureType.SecondaryStructureDssp.E) {
- return 'sheet'
- } else {
- return 'none'
- }
-}
-
-interface DSSPContext {
- /** Whether to use the old DSSP convention for the annotation of turns and helices, causes them to be two residues shorter */
- oldDefinition: boolean,
- /** alpha-helices are preferred over 3-10 helix */
- oldOrdering: boolean,
- getResidueFlag: (f: DSSPType) => SecondaryStructureType,
- getFlagName: (f: DSSPType) => String,
-
- hierarchy: AtomicHierarchy
- proteinResidues: SortedArray<ResidueIndex>
- /** flags for each residue */
- flags: Uint32Array
- hbonds: DsspHbonds,
-
- torsionAngles: { phi: number[], psi: number[]/*, omega: number[]*/ },
- backboneIndices: BackboneAtomIndices,
- conformation: AtomicConformation,
- ladders: Ladder[],
- bridges: Bridge[]
-}
-
-interface Ladder {
- previousLadder: number,
- nextLadder: number,
- firstStart: number,
- secondStart: number,
- secondEnd: number,
- firstEnd: number,
- type: BridgeType
-}
-
-const enum BridgeType {
- PARALLEL = 0x0,
- ANTI_PARALLEL = 0x1
-}
-
-class Bridge {
- partner1: number;
- partner2: number;
- type: BridgeType;
-
- constructor(p1: number, p2: number, type: BridgeType) {
- this.partner1 = Math.min(p1, p2)
- this.partner2 = Math.max(p1, p2)
- this.type = type
- }
-}
-
-type DSSPType = BitFlags<DSSPType.Flag>
-namespace DSSPType {
- export const is: (t: DSSPType, f: Flag) => boolean = BitFlags.has
- export const create: (f: Flag) => DSSPType = BitFlags.create
- export const enum Flag {
- _ = 0x0,
- H = 0x1,
- B = 0x2,
- E = 0x4,
- G = 0x8,
- I = 0x10,
- S = 0x20,
- T = 0x40,
- T3 = 0x80,
- T4 = 0x100,
- T5 = 0x200,
- T3S = 0x400, // marks 3-turn start
- T4S = 0x800,
- T5S = 0x1000
+ if (assignment === SecondaryStructureType.SecondaryStructureDssp.H || assignment === SecondaryStructureType.SecondaryStructureDssp.G || assignment === SecondaryStructureType.SecondaryStructureDssp.I) {
+ return 'helix'
+ } else if (assignment === SecondaryStructureType.SecondaryStructureDssp.B || assignment === SecondaryStructureType.SecondaryStructureDssp.E) {
+ return 'sheet'
+ } else {
+ return 'none'
}
}
-/** max distance between two C-alpha atoms to check for hbond */
-const caMaxDist = 9.0;
-
function calcAtomicTraceLookup3D(hierarchy: AtomicHierarchy, conformation: AtomicConformation) {
const { x, y, z } = conformation;
const { moleculeType, traceElementIndex } = hierarchy.derived.residue
@@ -284,7 +297,6 @@ function assignBends(ctx: DSSPContext) {
const caPosPrev2 = Vec3.zero()
const caPos = Vec3.zero()
const caPosNext2 = Vec3.zero()
- // let bends = 0
const nIndices = ctx.backboneIndices.nIndices
const cPos = Vec3.zero()
@@ -321,16 +333,14 @@ function assignBends(ctx: DSSPContext) {
const angle = Vec3.angle(caMinus2, caPlus2) * 360 / (2 * Math.PI)
if (angle && angle > 70.00) {
- // console.log(`found bend at ${ i } with kappa ${ angle }`)
flags[i] |= DSSPType.Flag.S
- // bends++
}
}
- // console.log(bends + ' bends')
}
function calculateDihedralAngles(hierarchy: AtomicHierarchy, conformation: AtomicConformation, proteinResidues: SortedArray<ResidueIndex>, backboneIndices: BackboneAtomIndices): { phi: number[], psi: number[]/*, omega: number[]*/ } {
const { cIndices, nIndices } = backboneIndices
+ const { index } = hierarchy
const { x, y, z } = conformation
const { traceElementIndex } = hierarchy.derived.residue
@@ -349,7 +359,6 @@ function calculateDihedralAngles(hierarchy: AtomicHierarchy, conformation: Atomi
const phi: number[] = []
const psi: number[] = []
- // const omega: number[] = []
for (let i = 0; i < residueCount - 1; ++i) {
const oPIprev = i - 1
@@ -370,7 +379,7 @@ function calculateDihedralAngles(hierarchy: AtomicHierarchy, conformation: Atomi
const nAtomNext = nIndices[oRInext]
// ignore C-terminal residue as acceptor
- // if (index.findAtomOnResidue(oRI, 'OXT') !== -1) continue
+ if (index.findAtomOnResidue(oRI, 'OXT') !== -1) continue
position(cAtomPrev, cPosPrev)
position(caAtomPrev, caPosPrev)
@@ -551,23 +560,6 @@ function getDSSPAssignment(flags: Uint32Array, getResidueFlag: (f: DSSPType) =>
return type as unknown as ArrayLike<SecondaryStructureType>
}
-/**
- * Constant for electrostatic energy in kcal/mol
- * f * q1 * q2
- * Q = -332 * 0.42 * 0.20
- *
- * f is the dimensional factor
- *
- * q1 and q2 are partial charges which are placed on the C,O
- * (+q1,-q1) and N,H (-q2,+q2)
- */
-const Q = -27.888
-
-/** cutoff for hbonds in kcal/mol, must be lower to be consider as an hbond */
-const hbondEnergyCutoff = -0.5
-
-const hbondEnergyMinimal = -9.9
-
/**
* E = Q * (1/r(ON) + l/r(CH) - l/r(OH) - l/r(CN))
*/
--
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